[med-svn] [Git][med-team/kmer][master] 7 commits: debhelper 11
Andreas Tille
gitlab at salsa.debian.org
Sun Aug 5 12:35:06 BST 2018
Andreas Tille pushed to branch master at Debian Med / kmer
Commits:
7d897abd by Andreas Tille at 2018-08-05T03:47:52Z
debhelper 11
- - - - -
9684aa8a by Andreas Tille at 2018-08-05T03:52:18Z
Point Vcs fields to salsa.debian.org
- - - - -
b182bacb by Andreas Tille at 2018-08-05T03:52:19Z
Standards-Version: 4.1.5
- - - - -
65485582 by Andreas Tille at 2018-08-05T05:20:32Z
Fix Perl interpreter path
- - - - -
2e9b7337 by Andreas Tille at 2018-08-05T09:01:22Z
Fix spelling
- - - - -
4129d4c8 by Andreas Tille at 2018-08-05T09:22:03Z
More paths to fix
- - - - -
3349d1f8 by Andreas Tille at 2018-08-05T09:34:45Z
More spelling issues
- - - - -
6 changed files:
- debian/changelog
- debian/compat
- debian/control
- debian/patches/series
- + debian/patches/spelling.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,14 @@
+kmer (0~20150903+r2013-4) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * debhelper 11
+ * Point Vcs fields to salsa.debian.org
+ * Standards-Version: 4.1.5
+ * Fix Perl interpreter path
+ * Fix spelling
+
+ -- Andreas Tille <tille at debian.org> Sun, 05 Aug 2018 05:47:52 +0200
+
kmer (0~20150903+r2013-3) unstable; urgency=medium
* Rename source package to match upstream name and primary binary package
=====================================
debian/compat
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-10
+11
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -3,15 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Afif Elghraoui <afif at debian.org>
Section: science
Priority: optional
-Build-Depends:
- debhelper (>= 10),
- dh-exec,
+Build-Depends: debhelper (>= 11~),
+ dh-exec,
# For ATAC
- dh-python,
- python-all-dev,
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/kmer.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/kmer.git
+ dh-python,
+ python-all-dev
+Standards-Version: 4.1.5
+Vcs-Browser: https://salsa.debian.org/med-team/kmer
+Vcs-Git: https://salsa.debian.org/med-team/kmer.git
Homepage: http://kmer.sourceforge.net
Package: kmer
@@ -20,7 +19,7 @@ Depends: ${misc:Depends},
meryl,
leaff,
sim4db,
- atac,
+ atac
Description: suite of tools for DNA sequence analysis
The kmer package is a suite of tools for DNA sequence analysis.
It provides tools for searching (ESTs, mRNAs, sequencing reads);
@@ -117,15 +116,14 @@ Description: batch spliced alignment of cDNA sequences to a target genome
Package: atac
Architecture: any
-Depends:
- ${shlibs:Depends},
- ${misc:Depends},
- ${python:Depends},
- ${perl:Depends},
- libfile-which-perl,
- leaff,
- meryl,
- gnuplot,
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ ${python:Depends},
+ ${perl:Depends},
+ libfile-which-perl,
+ leaff,
+ meryl,
+ gnuplot
Description: genome assembly-to-assembly comparison
atac computes a one-to-one pairwise alignment of large DNA sequences. It first
finds the unique k-mers in each sequence, chains them to larger blocks, and
=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
allow-freebsd-build.patch
atac-helper-script-paths.patch
atac-readme.patch
+spelling.patch
=====================================
debian/patches/spelling.patch
=====================================
--- /dev/null
+++ b/debian/patches/spelling.patch
@@ -0,0 +1,48 @@
+Description: Fix spelling
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sun, 05 Aug 2018 05:47:52 +0200
+
+--- a/libutil/bitPackedFile.C
++++ b/libutil/bitPackedFile.C
+@@ -157,7 +157,7 @@ bitPackedFile::bitPackedFile(char const
+ } else if ((at == uint64Swap(ac)) && (bt == uint64Swap(bc))) {
+ endianess_flipped = true;
+ } else {
+- fprintf(stderr, "bitPackedFile::bitPackedFile()-- '%s' looked like a bitPackedFile, but failed the endianess check, not opened.\n", _name);
++ fprintf(stderr, "bitPackedFile::bitPackedFile()-- '%s' looked like a bitPackedFile, but failed the endianness check, not opened.\n", _name);
+ exit(1);
+ }
+ } else {
+--- a/libkmer/driver-existDB.C
++++ b/libkmer/driver-existDB.C
+@@ -178,7 +178,7 @@ const char *usage =
+ "\n"
+ " -testexhaustive some.fasta some.meryl\n"
+ " -- Build an existDB table from some.fasta, check _EVERY_ mer\n"
+-" for existance. Complain if a mer exists in the table but\n"
++" for existence. Complain if a mer exists in the table but\n"
+ " not in the meryl database. Assumes 'some.meryl' is the\n"
+ " mercount of some.fasta.\n"
+ "\n";
+--- a/libutil/palloc.c
++++ b/libutil/palloc.c
+@@ -133,7 +133,7 @@ palloc2(size_t size, void *handle) {
+ root->_cn = root->_nl;
+
+ if (root->_dbg > 0)
+- fprintf(stderr, "palloc()-- Inital block of "sizetFMT" bytes at %p.\n", root->_bs, root->_cn);
++ fprintf(stderr, "palloc()-- Initial block of "sizetFMT" bytes at %p.\n", root->_bs, root->_cn);
+
+ root->_cn->_cp = 0;
+ root->_cn->_dt = (char *)really_allocate(root->_bs);
+--- a/sim4dbutils/parseSNP.C
++++ b/sim4dbutils/parseSNP.C
+@@ -491,7 +491,7 @@ main(int argc, char **argv) {
+ fprintf(stderr, " default, and if posTag is not found.\n");
+ fprintf(stderr, "\n");
+ fprintf(stderr, " TAGS: The number immediately after the first\n");
+- fprintf(stderr, " occurance of the tag will be used.\n");
++ fprintf(stderr, " occurrence of the tag will be used.\n");
+ fprintf(stderr, "\n");
+ fprintf(stderr, " -o offset An additive offset to the SNP position.\n");
+ fprintf(stderr, " The default is 0.\n");
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -34,5 +34,11 @@ override_dh_auto_clean:
$(MAKE) real-clean
rm -rf installdir
+override_dh_install:
+ dh_install
+ for perlscript in `grep -l '#!/usr/bin/env \+perl' debian/*/usr/bin/*` `grep -l '#!/usr/bin/env \+perl' debian/*/usr/lib/atac/bin/*` ; do \
+ sed -i '1s+#!/usr/bin/env perl+#!/usr/bin/perl+' $${perlscript} ; \
+ done
+
get-orig-source:
DEB_VERSION_UPSTREAM=$(DEB_VERSION_UPSTREAM) debian/get-orig-source
View it on GitLab: https://salsa.debian.org/med-team/kmer/compare/de16f7df09c5ba18ca28af09269c8ef3bc61968e...3349d1f8dd802f85f27e588919f2274cf115098d
--
View it on GitLab: https://salsa.debian.org/med-team/kmer/compare/de16f7df09c5ba18ca28af09269c8ef3bc61968e...3349d1f8dd802f85f27e588919f2274cf115098d
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